The school has to have a doctor's note in order to be able to exempt him in any way, shape, or form, from PE or any other class. Once the doctor releases him to go back to school with limitations, you can talk that over with the guidance office at the school, since they are responsible for working with administrators to ensure that student schedules are adequate.

If his headaches are still bad, I can't see how going back to school will help, unless he can manage them with sun glasses and ear plugs to reduce the impact of bright lights and loud noises... but then he would need a doctor's note for the glasses, and honestly I have known several teens who were supposed to follow similar instructions for a variety of reasons and refused to do so because they didn't want to draw unwanted attention from their peers (you know how it is... teens think everything revolves around them lol). I don't know your son, but just from my experiences I would would push himself and just make his symptoms worse.

Maybe you could convince the doctor to let him go back for half days, if the school can work out his schedule to make that plausible?